Mercurial > repos > nml > bio_hansel
annotate bio_hansel.xml @ 8:e9fd173fc7ee draft
planemo upload for repository https://github.com/phac-nml/bio_hansel commit df5241c32e2350d7ac49d546a0e390e1ef892c96
author | nml |
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date | Fri, 20 Apr 2018 10:44:35 -0400 |
parents | af59ac462926 |
children | 4654c51dae72 |
rev | line source |
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8
e9fd173fc7ee
planemo upload for repository https://github.com/phac-nml/bio_hansel commit df5241c32e2350d7ac49d546a0e390e1ef892c96
nml
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1 <tool id="bio_hansel" name="Bio Hansel" version="1.3.1"> |
3
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
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2 <description>SNV Subtyping with genome assemblies or reads</description> |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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3 <requirements> |
8
e9fd173fc7ee
planemo upload for repository https://github.com/phac-nml/bio_hansel commit df5241c32e2350d7ac49d546a0e390e1ef892c96
nml
parents:
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4 <requirement type="package" version="1.3.1">bio_hansel</requirement> |
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9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
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5 <requirement type="package" version="17.2.0">attrs</requirement> |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
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6 </requirements> |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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7 <command detect_errors="exit_code"><![CDATA[ |
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ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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8 ## Preparing file input. |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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9 #if $data_type.type == "paired": |
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9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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10 |
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6396d043667b
planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
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11 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq && |
6396d043667b
planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
nml
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12 ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name'.fastq && |
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ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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13 |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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14 #elif $data_type.type == "collection": |
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9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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15 |
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6396d043667b
planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
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16 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq && |
6396d043667b
planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
nml
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17 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq && |
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9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
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diff
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18 |
1
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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19 #elif $data_type.type == "single": |
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9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
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20 |
1
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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21 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): |
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6396d043667b
planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
nml
parents:
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22 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq && |
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9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
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23 #end if |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
diff
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24 |
1
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
parents:
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25 #if $data_type.fastq_input1.is_of_type('fasta'): |
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6396d043667b
planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
nml
parents:
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26 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fasta && |
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9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
diff
changeset
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27 #end if |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
diff
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28 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
diff
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29 #end if |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
diff
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30 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
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31 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
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32 ## Checking for custom scheme. |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
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33 #if $type_of_scheme.scheme_type == "custom": |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
diff
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34 #if $type_of_scheme.scheme_input.is_of_type('fasta'): |
1
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
parents:
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35 ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' && |
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9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
diff
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36 #end if |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
diff
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37 #end if |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
diff
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38 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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39 ## Start the actual command here |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
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40 hansel |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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parents:
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41 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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42 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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43 ## Select the scheme |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
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44 -s |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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45 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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46 #if $type_of_scheme.scheme_type == "heidelberg": |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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47 heidelberg |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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48 #elif $type_of_scheme.scheme_type == "enteritidis": |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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49 enteritidis |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
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50 #elif $type_of_scheme.scheme_type == "custom": |
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ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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51 '$type_of_scheme.scheme_input.name' |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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52 #end if |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
parents:
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53 |
5
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
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54 ## Use Json output |
6396d043667b
planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
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55 #if $dev_args.use_json == "yes": |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit e04f7d6043451f66946394d5a14582a1b39a6ec7-dirty
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56 --json |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
nml
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57 #end if |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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parents:
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58 |
3
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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59 #if $kmer_vals.kmer_min |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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60 --min-kmer-freq $kmer_vals.kmer_min |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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61 #end if |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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62 |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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63 #if $kmer_vals.kmer_max |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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64 --max-kmer-freq $kmer_vals.kmer_max |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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65 #end if |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
nml
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66 |
3
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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67 #if $qc_vals.low_cov_depth_freq |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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68 --low-cov-depth-freq $qc_vals.low_cov_depth_freq |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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69 #end if |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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70 |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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71 #if $qc_vals.max_missing_tiles |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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72 --max-missing-tiles $qc_vals.max_missing_tiles |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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73 #end if |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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74 |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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75 #if $qc_vals.min_ambiguous_tiles |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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76 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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77 #end if |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
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78 |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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79 #if $qc_vals.max_intermediate_tiles |
29faaa849e41
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
nml
parents:
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80 --max-intermediate-tiles $qc_vals.max_intermediate_tiles |
0
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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81 #end if |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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parents:
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82 |
6
5a42e475436e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit e04f7d6043451f66946394d5a14582a1b39a6ec7-dirty
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83 #if $qc_vals.low_coverage_warning |
5a42e475436e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit e04f7d6043451f66946394d5a14582a1b39a6ec7-dirty
nml
parents:
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84 --low-cov-warning $qc_vals.low_coverage_warning |
5a42e475436e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit e04f7d6043451f66946394d5a14582a1b39a6ec7-dirty
nml
parents:
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85 #end if |
5a42e475436e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit e04f7d6043451f66946394d5a14582a1b39a6ec7-dirty
nml
parents:
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86 |
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87 ## Adding more parameters to the command. |
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88 -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab |
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89 |
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90 |
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91 ## Entering the file inputs |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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92 |
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93 #if $data_type.type == "single": |
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94 |
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95 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): |
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96 '$data_type.fastq_input1.name'.fastq |
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97 #end if |
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98 |
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99 #if $data_type.fastq_input1.is_of_type('fasta'): |
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100 '$data_type.fastq_input1.name'.fasta |
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101 #end if |
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102 |
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103 #elif $data_type.type =="collection": |
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104 -p '$data_type.fastq_input1.name'_1.fastq '$data_type.fastq_input1.name'_2.fastq |
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105 |
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106 #elif $data_type.type =="paired": |
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107 -p '$data_type.fastq_input1.name'.fastq '$data_type.fastq_input2.name'.fastq |
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108 #end if |
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109 |
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110 ]]></command> |
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111 <inputs> |
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112 <conditional name="data_type"> |
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113 <param name="type" type="select" label="Specify the read type."> |
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114 <option value="single">Single-end Data</option> |
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115 <option value="paired">Paired-end Data</option> |
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116 <option value="collection">Collection Paired-end Data</option> |
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117 </param> |
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118 <when value="single"> |
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119 <param name="fastq_input1" type="data" format="fastqsanger, fastq, fasta" label="Single end read file(s)"/> |
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120 </when> |
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121 <when value="paired"> |
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122 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/> |
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123 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/> |
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124 </when> |
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125 <when value="collection"> |
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126 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" /> |
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127 </when> |
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128 </conditional> |
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129 <conditional name="type_of_scheme"> |
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130 <param name="scheme_type" type="select" label="Specify scheme to use. (Heidelberg is default)"> |
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131 <option value="heidelberg">Heidelberg scheme</option> |
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132 <option value="enteritidis">Enteritidis scheme</option> |
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133 <option value="custom">Specify your own custom scheme</option> |
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134 </param> |
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135 <when value="heidelberg"/> |
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136 <when value="enteritidis"/> |
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137 <when value="custom"> |
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138 <param name="scheme_input" type="data" format="fasta" label="Scheme Input"/> |
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139 </when> |
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140 </conditional> |
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141 <!-- K-mer frequencies. --> |
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142 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False"> |
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143 <param name="kmer_min" argument="--min-kmer-freq" optional="True" type="integer" min="0" label="Min k-mer freq/coverage" value="8" help="default = 8"/> |
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144 <param name="kmer_max" argument="--max-kmer-freq" optional="True" type="integer" min="1" label="Max k-mer freq/coverage" value="1000" help="default = 1000"/> |
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145 </section> |
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146 <!-- Quality Checking Parameters --> |
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147 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False"> |
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148 <param name="low_cov_depth_freq" argument="--low-cov-depth-freq" optional="True" type="integer" min="0" label="QC: Frequency below this coverage are considered low coverage" value="20" help="default = 20"/> |
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149 <param name="min_ambiguous_tiles" argument="--min-ambiguous-tiles" optional="True" type="integer" min="0" label="QC: Min number of tiles missing for Ambiguous Result" value="3" help="default = 3"/> |
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150 <param name="max_missing_tiles" argument="--max-missing-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> |
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151 <param name="max_intermediate_tiles" argument="--max-intermediate-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> |
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152 <param name="low_coverage_warning" argument="--low-cov-warning" optional="True" type="integer" min="0" label="QC: Overall tile coverage below this value will trigger a low coverage warning" value="20" help="default = 20"/> |
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153 </section> |
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154 <section name="dev_args" title="Developer Options" expanded="False"> |
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155 <param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details"> |
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156 <option value="no">no</option> |
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157 <option value="yes">yes</option> |
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158 </param> |
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159 </section> |
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160 </inputs> |
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161 <outputs> |
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162 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/> |
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163 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/> |
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164 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/> |
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165 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json"> |
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166 <filter>dev_args['use_json'] == "yes"</filter> |
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167 </data> |
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168 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json"> |
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169 <filter>dev_args['use_json'] == "yes"</filter> |
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170 </data> |
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171 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json"> |
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172 <filter>dev_args['use_json'] == "yes"</filter> |
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173 </data> |
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174 </outputs> |
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175 <tests> |
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176 <test> |
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177 <param name="type" value="single"/> |
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178 <param name="type_of_scheme" value="heidelberg"/> |
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179 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/> |
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180 <output name="results.tab"> |
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181 <assert_contents> |
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182 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/> |
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183 </assert_contents> |
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184 </output> |
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185 <output name="match_results.tab"> |
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186 <assert_contents> |
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187 <has_text_matching expression="tilename\s+seq\s+is_revcomp\s+contig_id\s+match_index\s+refposition\s+subtype\s+is_pos_tile\s+sample\s+file_path\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/> |
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188 </assert_contents> |
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189 </output> |
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190 <output name="tech_results.tab"> |
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191 <assert_contents> |
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192 <has_text_matching expression="sample\s+subtype\s+qc_status\s+qc_message"/> |
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193 </assert_contents> |
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194 </output> |
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195 </test> |
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196 <test> |
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197 <param name="type" value="paired"/> |
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198 <param name="type_of_scheme" value="heidelberg"/> |
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199 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/> |
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200 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/> |
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201 <output name="results.tab"> |
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202 <assert_contents> |
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203 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+avg_tile_coverage\s+qc_status\s+qc_message"/> |
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204 </assert_contents> |
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205 </output> |
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206 <output name="match_results.tab"> |
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207 <assert_contents> |
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208 <has_text_matching expression="tilename\s+seq\s+freq\s+refposition\s+subtype\s+is_pos_tile\s+is_kmer_freq_okay\s+sample\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/> |
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209 </assert_contents> |
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210 </output> |
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211 <output name="tech_results.tab"> |
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212 <assert_contents> |
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213 <has_text_matching expression="sample\s+subtype\s+avg_tile_coverage\s+qc_status\s+qc_message"/> |
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214 </assert_contents> |
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215 </output> |
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216 </test> |
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217 </tests> |
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218 <help><![CDATA[ |
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219 *********************************************************** |
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220 bio_hansel - Heidelberg And eNteritidis Snp ELucidation |
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221 *********************************************************** |
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222 |
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223 Subtype *Salmonella enterica* subsp. enterica serovar Heidelberg and Enteritidis genomes using *in-silico* 33 bp k-mer SNP subtyping schemes developed by Genevieve Labbe et al. |
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224 Subtype *Salmonella* genome assemblies (FASTA files) and/or whole-genome sequencing reads (FASTQ files)! |
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225 |
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226 Usage |
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227 ===== |
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228 1) Enter your FASTA/FASTQ file(s) |
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229 2) Select which scheme you would like to use (e.g. heidelberg, enteritidis, or specify your own) |
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230 3) Click Execute |
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231 |
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232 For more information visit `https://github.com/phac-nml/bio_hansel` |
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233 |
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234 |
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235 Example Usage |
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236 ============= |
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237 |
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238 Analysis of a single FASTA file |
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239 ------------------------------- |
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240 |
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241 |
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242 Contents of ``results.tab``: |
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243 |
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244 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+ |
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245 | sample | scheme | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_total | n_tiles_matching_positive | n_tiles_matching_positive_total | n_tiles_matching_subtype | n_tiles_matching_subtype_total | file_path | |
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246 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+ |
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247 | file.fasta | heidelberg | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 1037658-2.2.2.2.1.4; 2154958-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | file.fasta | |
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248 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+ |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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249 |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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250 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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251 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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252 Contents of ``match_results.tab``: |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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253 |
1
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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254 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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255 | tilename | stitle | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | qlen | slen | seq | coverage | is_trunc | refposition | subtype | is_pos_tile | sample | file_path | scheme | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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256 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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257 | 775920-2.2.2.2 | NODE_2_length_512016_cov_46.4737_ID_3 | 100 | 33 | 0 | 0 | 1 | 33 | 474875 | 474907 | 2E-11 | 62.1 | 33 | 512016 | GTTCAGGTGCTACCGAGGATCGTTTTTGGTGCG | 1 | False | 775920 | 2.2.2.2 | True | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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258 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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259 | negative3305400-2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 276235 | 276267 | 2E-11 | 62.1 | 33 | 427905 | CATCGTGAAGCAGAACAGACGCGCATTCTTGCT | 1 | False | negative3305400 | 2.1.1.1 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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260 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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261 | negative3200083-2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 170918 | 170950 | 2E-11 | 62.1 | 33 | 427905 | ACCCGGTCTACCGCAAAATGGAAAGCGATATGC | 1 | False | negative3200083 | 2.1 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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262 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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263 | negative3204925-2.2.3.1.5 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 175760 | 175792 | 2E-11 | 62.1 | 33 | 427905 | CTCGCTGGCAAGCAGTGCGGGTACTATCGGCGG | 1 | False | negative3204925 | 2.2.3.1.5 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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264 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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265 | negative3230678-2.2.2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 201513 | 201545 | 2E-11 | 62.1 | 33 | 427905 | AGCGGTGCGCCAAACCACCCGGAATGATGAGTG | 1 | False | negative3230678 | 2.2.2.1.1.1 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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266 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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267 | negative3233869-2.1.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 204704 | 204736 | 2E-11 | 62.1 | 33 | 427905 | CAGCGCTGGTATGTGGCTGCACCATCGTCATTA | 1 | False | negative3233869 | 2.1.1.1.1 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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268 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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269 | negative3254229-2.2.3.1.3 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 225064 | 225096 | 2E-11 | 62.1 | 33 | 427905 | CGCCACCACGCGGTTAGCGTCACGCTGACATTC | 1 | False | negative3254229 | 2.2.3.1.3 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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270 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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271 | negative3257074-2.2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 227909 | 227941 | 2E-11 | 62.1 | 33 | 427905 | CGGCAACCAGACCGACTACGCCGCCAAGCAGAC | 1 | False | negative3257074 | 2.2.1 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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272 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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273 | negative3264474-2.2.2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 235309 | 235341 | 2E-11 | 62.1 | 33 | 427905 | AATGGCGCCGATCGTCGCCAGATAACCGTTGCC | 1 | False | negative3264474 | 2.2.2.1.1.1 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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274 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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275 | negative3267927-2.2.2.2.2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 238762 | 238794 | 2E-11 | 62.1 | 33 | 427905 | AAAGAGAAATATGATGCCAGGCTGATACATGAC | 1 | False | negative3267927 | 2.2.2.2.2.1 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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276 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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277 | negative3278067-1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 248902 | 248934 | 2E-11 | 62.1 | 33 | 427905 | TGTGAGTAAGTTGCGCGATATTCTGCTGGATTC | 1 | False | negative3278067 | 1.1 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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278 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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279 | negative3299717-2.2.3.1.4 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 270552 | 270584 | 2E-11 | 62.1 | 33 | 427905 | ATGCCGGACAGCAGGCGAAACTCGAACCGGATA | 1 | False | negative3299717 | 2.2.3.1.4 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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280 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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281 | negative3373069-2.2.2.2.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 344011 | 344043 | 2E-11 | 62.1 | 33 | 427905 | CTCTCCAGAAGATGAAGCCCGTGATGCGGCGCA | 1 | False | negative3373069 | 2.2.2.2.1.1 | False | out | file.fasta | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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282 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ |
0
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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283 |
1
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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284 Next 196 lines omitted. |
0
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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285 |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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286 |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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287 |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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288 Analysis of a single FASTQ readset |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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289 ---------------------------------- |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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290 |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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291 Contents of ``results.tab``: |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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292 |
1
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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293 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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294 | sample | scheme | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_total | n_tiles_matching_positive | n_tiles_matching_positive_total | n_tiles_matching_subtype | n_tiles_matching_subtype_total | file_path | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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295 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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296 | 564 | heidelberg | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | forward.fastqsanger; reverse.fastqsanger | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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297 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+ |
0
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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298 |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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299 |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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300 Contents of ``match_results.tab``: |
9407a9eaad22
planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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301 |
1
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302 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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303 | seq | freq | sample | file_path | tilename | is_pos_tile | subtype | refposition | is_kmer_freq_okay | scheme | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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304 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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305 | ACGGTAAAAGAGGACTTGACTGGCGCGATTTGC | 68 | 564 | forward.fastqsanger; reverse.fastqsanger | 21097-2.2.1.1.1 | True | 2.2.1.1.1 | 21097 | True | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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306 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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307 | AACCGGCGGTATTGGCTGCGGTAAAAGTACCGT | 77 | 564 | forward.fastqsanger; reverse.fastqsanger | 157792-2.2.1.1.1 | True | 2.2.1.1.1 | 157792 | True | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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308 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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309 | CCGCTGCTTTCTGAAATCGCGCGTCGTTTCAAC | 67 | 564 | forward.fastqsanger; reverse.fastqsanger | 293728-2.2.1.1 | True | 2.2.1.1 | 293728 | True | heidelberg | |
ba271365095e
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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310 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ |
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planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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311 | GAATAACAGCAAAGTGATCATGATGCCGCTGGA | 91 | 564 | forward.fastqsanger; reverse.fastqsanger | 607438-2.2.1 | True | 2.2.1 | 607438 | True | heidelberg | |
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312 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ |
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313 | CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA | 87 | 564 | forward.fastqsanger; reverse.fastqsanger | 691203-2.2.1.1 | True | 2.2.1.1 | 691203 | True | heidelberg | |
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314 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ |
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315 | CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC | 33 | 564 | forward.fastqsanger; reverse.fastqsanger | 944885-2.2.1.1.1 | True | 2.2.1.1.1 | 944885 | True | heidelberg | |
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316 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ |
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317 |
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318 Next 200 lines omitted. |
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319 |
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320 Galaxy wrapper written by Matthew Gopez at the Public Health Agency of Canada, National Microbiology Laboratory. |
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321 |
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322 ]]></help> |
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323 <citations> |
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324 <citation type="bibtex">@ARTICLE{a1, |
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325 title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.}, |
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326 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash.}, |
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327 url = {https://github.com/phac-nml/bio_hansel} |
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328 } |
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329 }</citation> |
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330 </citations> |
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331 </tool> |